butene and acetanilide: learning to use webmo - bluffton

2Butene and Acetanilide: learning to use WebMO WebMO is a browser-based Java interface to a number of popular computational chemistry programs. The interface works the same for all such programs; the program we will use is Gaussian.

WebMO is provided for academic use in Ohio by the Ohio Supercomputer Center.

To log into WebMO, go to https://webmo.osc.edu. Your username is your last name and first initial (all lower-case), and your password is the last four digits of your student ID number. For example, John Smith (ID # 12345) logs in as “smithj” and his password is “2345”.

Your student accounts will be deleted at the end of this semester; if you need to use WebMO for research or other Bluffton-related purposes, please contact Dr. Berger for an account.

NH CH3

O

acetanilide

CH3

CH3CH3CH3

cis and trans 2-butene

Follow the instructions on the following pages to build the structures and examine their properties.

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Building cis‐ and trans‐2‐butene

• Go to https://webmo osc eduhttps://webmo.osc.edu

• Log into WebMO with your username and password


• You will now be in the Job Manager. The first time you log in it will look like this.

• Select “New Job”

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• The “Build Molecule” window will openwindow will open.

• Select “Open Editor.”


• The Editor is a separate window.window.

• The Editor defaults to Build Mode – C (building carbon atoms).

• Click in the window four i l ftimes to place four carbon atoms in a cisarrangement.

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• Now click on the first atom and drag to theatom and drag to the second.

• Click on the second and drag to the third.

• Click on the third and drag to the fourth

• You will have placed bonds between the four atoms.


• Click on the “pointer” button (“Adjust”) in thebutton ( Adjust ) in the tool menu.

• Right‐click on the middle bond, and select “Double” from the menu that appearsmenu that appears.

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• Click the “Wrench” tool (“Comprehensive( Comprehensive Cleanup using Mechanics”).

• The “Broom” tool (“Comprehensive Cleanup”) will alsoCleanup ) will also work.


• You have successfully built cis 2 butenebuilt cis‐2‐butene.

• Click on the “eXit” button to go back to the Build Molecule window.

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• Now you are ready to create your jobto create your job.

• Click the “Right Arrow” button to go on to the next step.


• Name your job “cis 2 butene”cis‐2‐butene .

• Change “Calculation” to “Geometry Optimization”

• Change “Theory”• Change Theory to “AM1”

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• Click the “Right Arrow” button toArrow button to submit your calculation to the server.


• You will go to the Job Manager. When your job is complete, the Job Manager will update to show that it is complete.

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• Repeat these steps to build trans‐2‐butene.

• Be sure you place your four carbon atoms in a “zig‐zag” configuration.

• If you use the “Broom” tool to clean up rather than the “Wrench” tool, you may get cis again. Ifyou may get cis again. If so, select “Undo” from the Edit menu and try the “Wrench” tool.


• We will now examine our 2‐butene isomers.

• Click on the “View Job” button at the far right, for one of the two jobs.

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• Scroll down in the window and recordwindow, and record the “AM1 Energy.”

• View the other butene calculation and record its energyenergy.

• How do the two compare?

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Building acetanilide in WebMO

• Using the menu at left, click “Job Manager”click Job Manager.

• Start a new job and open the Editor.

• Within the Editor, select the “Build” menu and choose “Fragment ”choose Fragment.


1. Under “Category” select “Rings ”select Rings.

2. Under “Fragment” select “Benzene.”

3. Click “OK.”

4. Click in the Editor i d l

1

23

4window to place a benzene molecule there.

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• Acetanilide has an acetamido groupacetamido group attached to benzene.

• Use the “View” tools to adjust the size and position of the molecule so that youmolecule so that you have room to build.


• Click the “Build” button.

Cli k f th• Click on one of the hydrogen atoms to change it to a carbon atom.

• Place three more atoms in the window and

12

3

in the window and connect them as shown.

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• Click the periodic table button A dialogbutton. A dialog window will open.


• Click “N” for nitrogen.

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• Click the carbon atom indicated by the blueindicated by the blue arrow, to change it to nitrogen.

• Now, using the periodic table button, change to oxygen and convert theoxygen and convert the carbon atom indicated by the red arrow.


1. Right‐click to change the bond indicated to

3

the bond indicated to a double bond.

2. Click the Broom button (“Comprehensive Cleanup”).

3 Close the Editor

1

3. Close the Editor window.

2

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• Click the right‐arrow button, and name the job “Acetanilide.” Use the same parameters as before (as above).

• Click the right‐arrow button again to submit the job.


• When the job is finished, the Job Manager will show it as “Complete ”it as Complete.

• Click “View Job” for your acetanilide structure.

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• We will now examine the molecular orbitals and electrostatic potential map (charge map) of acetanlide.

• Click “New Job Using This Geometry.” Click the right‐arrow button to reach the “Configure Guassian” window.


• Set up the parameters as shown at left:as shown at left:

– Acetanilide

– Molecular Orbitals

– AM1

– 00

– Singlet

• Click the right arrow to submit the job.

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• When the job is completed click “Viewcompleted, click View job”.

• Scroll down to molecular orbital 26, and select “View”.

• A new window will• A new window will open. Be patient while it loads.


• The selected Molecular Orbital is shown in theOrbital is shown in the window.

• You can view other orbitals by click on them in the menu at the leftthe left.

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• To see the electrostatic potential surface clickpotential surface, click the labeled bar.

• If you have a three‐button mouse, drag the middle button to resize.

• If you have a scroller• If you have a scrollermouse, use the scrollerto resize.


• To make the surface more transparentmore transparent, select “Edit MOViewerPreferences.”

• Change “Opacity” to 66% or less.

• Click “Apply” or “OK ”• Click Apply or OK.

• Exit the window when you are done.

butene and acetanilide: learning to use webmo - bluffton

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